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- PDB-6ags: Structural insights for non-natural cofactor binding by the L310R... -

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Basic information

Entry
Database: PDB / ID: 6ags
TitleStructural insights for non-natural cofactor binding by the L310R/Q401C mutant of malic enzyme from Escherichia coli
ComponentsNAD-dependent malic enzyme
KeywordsOXIDOREDUCTASE / Malic Enzyme
Function / homology
Function and homology information


malate dehydrogenase (oxaloacetate-decarboxylating) / malate dehydrogenase (decarboxylating) (NAD+) activity / malic enzyme activity / oxaloacetate decarboxylase activity / malate metabolic process / pyruvate metabolic process / gluconeogenesis / NAD binding / metal ion binding / cytosol
Similarity search - Function
NAD-dependent malic enzyme, proteobacteria / Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain ...NAD-dependent malic enzyme, proteobacteria / Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain / Malic enzyme, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / NAD-dependent malic enzyme
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsLiu, Y.X. / Liu, W.J. / Ji, D.B. / Zhao, K.
CitationJournal: Chembiochem / Year: 2021
Title: Structural Insights into Malic Enzyme Variants Favoring an Unnatural Redox Cofactor.
Authors: Liu, Y. / Guo, X. / Liu, W. / Wang, J. / Zhao, Z.K.
History
DepositionAug 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent malic enzyme


Theoretical massNumber of molelcules
Total (without water)64,3481
Polymers64,3481
Non-polymers00
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24120 Å2
Unit cell
Length a, b, c (Å)80.570, 80.570, 209.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-767-

HOH

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Components

#1: Protein NAD-dependent malic enzyme / NAD-ME


Mass: 64348.234 Da / Num. of mol.: 1 / Mutation: L310R, Q401C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: maeA, ECWI2_2348 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1X7B3B3, UniProt: P26616*PLUS, malate dehydrogenase (oxaloacetate-decarboxylating)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.7 M Lithium chloride,0.1 M Citric acid pH 4.6, 7% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.988 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 47534 / % possible obs: 99.8 % / Redundancy: 13.4 % / Net I/σ(I): 26.1
Reflection shellResolution: 2→2.04 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 1.6 / Rpim(I) all: 0.344 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AW5

2aw5


Resolution: 2.31→40.32 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.855 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.225 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24389 1576 5 %RANDOM
Rwork0.19743 ---
obs0.19973 29682 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.799 Å2
Baniso -1Baniso -2Baniso -3
1-3.04 Å20 Å20 Å2
2--3.04 Å20 Å2
3----6.08 Å2
Refinement stepCycle: 1 / Resolution: 2.31→40.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4377 0 0 200 4577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194464
X-RAY DIFFRACTIONr_bond_other_d0.0010.024282
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.9626057
X-RAY DIFFRACTIONr_angle_other_deg0.8539830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1415556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86924.507213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24115766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9631532
X-RAY DIFFRACTIONr_chiral_restr0.0960.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215118
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021026
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.1966.4192227
X-RAY DIFFRACTIONr_mcbond_other5.1956.4182226
X-RAY DIFFRACTIONr_mcangle_it7.489.6082781
X-RAY DIFFRACTIONr_mcangle_other7.4799.612782
X-RAY DIFFRACTIONr_scbond_it5.5296.9852237
X-RAY DIFFRACTIONr_scbond_other5.5266.9852237
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.16610.2823276
X-RAY DIFFRACTIONr_long_range_B_refined10.81251.4655213
X-RAY DIFFRACTIONr_long_range_B_other10.82151.4665140
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.305→2.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 104 -
Rwork0.249 2003 -
obs--92.53 %

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